He directed the excavation of one of the wonders of the American West, Pueblo Bonito, the 800-room Native American brick complex built 1200 years ago in the Arizona desert.

Barely a year or two earlier, Hubbard, a Tottenville native, had been excavating Indian shell heaps, middens and gravesites on South Shore beaches, publishing his findings in Proceedings, the scholarly journal of the Staten Island Museum in St. George.

The experience undoubtedly helped prepare him for Pueblo Bonito. He became associated with several of the towering figures in the field, including collector George Gustav Heye. (The Customs House branch of the National Museum of the American Indian in lower Manhattan is called the George Gustav Heye Center).

Somehow the apparently quiet and self-effacing Pepper never won the fame his work ought to have brought him. That may be changing.

A big exhibit of his collections (textiles, pottery, jewelry), photographs and writing — “Ancestors and Descendants: Ancient Southwestern America at the Dawn of the Twentieth Century” — opened earlier this summer at the New Orleans Museum of Art.

The NOMA show’s curator, Paul Tarver, thinks a Hubbard re-evaluation is imminent. Scholars and graduate students are “discovering” him. Next month, the Heye Center will show 1,000-year-old objects that Pepper recovered in Ecuador and Arizona.

“Something is in the wind,” Tarver said.

As one point, Tarver was himself under-informed about Pepper, although he was well aware of the Pueblo Bonito excavations in the 1890s.

Then, two years ago, he was invited to look through a relatively obscure collection of artifacts, photographs and documents given to Tulane University by Pepper’s widow.

It was valuable stuff. At one point he pulled out a glass lantern slide in which four Hopi Indian boys are applying their palm prints to an ancient cliff wall in Chaco Canyon.

It looks merely charming to laymen. But to someone in the field, the photograph tells a whole story of the indigenous culture of the southwest presenting the boys as descendants and heirs of the long-gone Pueblo Bonito people. It’s on the cover of the catalogue of “Ancestors and Descendants.” Pepper, who worked for the American Museum of Natural History for much of his life, collected material related to the present-day inhabitants of the Arizona desert — the Hopi and Navaho people.

He studied their weaving, pottery and jewelry-making, their rituals and dances, just as the traditional practices were being modified — contaminated — by the tourist trade. His photographed the Hopi Snake Dance, an amazing tradition that has been off-limits to outsiders for a hundred years now.

In the elaborate run-up to the dance, snake hunters collect dozens of sidewinders — mostly rattlers — from the four directions. Later, snake priests will dance, holding their snake “partners” in their mouths or fingers. They believe that properly supplicated, the snakes can summon rain.

Pepper’s Indiana Jones moment came in the snake pit. He was so comfortable with snakes the Navaho called him “Hostine Klish (Snake Man).” Whenever excavators encountered peevish reptiles, Pepper would be summoned to remove them.

Museum explorers were expected to give illustrated talks to women’s clubs and other groups eager for such presentations. Pepper spoke extemporaneously and used hand-tinted, glass lantern slides. Many ended up in the Tulane collection and are shown in “Ancestors and Descendants.”

Unlike some of his colleagues, Pepper apparently fell in love with his subjects and their world. For a 1903 lecture he wrote: “It is with no small degree of pleasure that I come before you to speak of a land that I have learned to love and of the people who are its children. Savages some call them but to me they are friends.

Pepper was living in Manhattan when he died at 51, reportedly of a renal disorder. It has been suggested that the cause was years of drinking bad water in the desert. At the time, objects he found/collected/preserved had made their way into public and private collections across the country.

Just months after his death, his widow, Jesse Crellin Pepper, purchased a house in Tottenville (95 Bentley St.) from her husband’s brother, Dewitt, for the kindhearted sum of “$1 lawful money.”